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Title: Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area

Abstract

The particulate and biological components of indoor air have a substantial impact on human health, especially immune respiratory conditions such as asthma. To better explore the relationship between allergens, the microbial community, and the indoor living environment, we sampled the bedrooms of 65 homes in the Chicago area using 23the patient-friendly Inspirotec electrokinetic air sampling device, which collects airborne particles for characterization of both allergens and microbial DNA. The sampling device captured sufficient microbial material to enable 16S rRNA amplicon sequencing data to be generated for every sample in the study. Neither the presence of HEPA filters nor the height at which the air sampling device was placed had any influence on the microbial community profile. A core microbiota of 31 OTUs was present in more than three quarters of the samples, comprising around 45% of the relative sequence counts in each bedroom. The most abundant single organisms were Staphylococcus, with other core taxa both human and outdoor-associated. Bacterial alpha diversity was significantly increased in bedrooms that reported having open windows, those with flowering plants in the vicinity, and those in homes occupied by dogs. Porphyromonas, Moraxella, Sutterella, and Clostridium, along with family Neisseraceae, were significantly enriched in homes withmore » dogs; interestingly, cats did not show a significant impact on microbial diversity or relative abundance. While dog allergen load was significantly correlated with bacterial alpha diversity, the taxa that significantly correlated with allergen burden did not exclusively overlap with those enriched in homes with dogs. Alternaria allergen load was positively correlated with bacterial alpha diversity, while Aspergillus allergen load was negatively correlated. The Alternaria allergen load was also significantly correlated with open windows. Microbial communities were significantly differentiated between rural, suburban, and urban homes and houses that were physically closer to each other maintained significantly more similar microbiota. We have demonstrated that it is possible to determine significant associations between allergen burden and the microbiota in air from the same sample and that these associations relate to the characteristics of the home and neighborhoods.« less

Authors:
ORCiD logo [1];  [2];  [2];  [3];  [3];  [3];  [4]
+ Show Author Affiliations
  1. Columbia Univ., New York, NY (United States). Dept. of Systems Biology; Columbia Univ., New York, NY (United States). Integrated Program in Cellular, Molecular, and Biomedical Studies; Univ. of Chicago, IL (United States). Dept. of Surgery. The Microbiome Center
  2. Univ. of Chicago, IL (United States). Dept. of Surgery. The Microbiome Center; The Scripps Research Inst., La Jolla, CA (United States). Scripps Inst. of Oceanography; Univ. of California, San Diego, CA (United States). Dept. of Pediatrics; Argonne National Lab. (ANL), Argonne, IL (United States). BioScience Division
  3. Inspirotec Inc., Chicago, IL (United States)
  4. Univ. of Chicago, IL (United States). Dept. of Surgery. The Microbiome Center; Argonne National Lab. (ANL), Argonne, IL (United States). BioScience Division; Univ. of Illinois, Chicago, IL (United States). Dept. of Biological Sciences
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1627052
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Microbiology

Citation Formats

Richardson, Miles, Gottel, Neil, Gilbert, Jack A., Gordon, Julian, Gandhi, Prasanthi, Reboulet, Rachel, and Hampton-Marcell, Jarrad T. Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area. United States: N. p., 2019. Web. doi:10.1186/s40168-019-0695-5.
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Richardson, Miles, Gottel, Neil, Gilbert, Jack A., Gordon, Julian, Gandhi, Prasanthi, Reboulet, Rachel, & Hampton-Marcell, Jarrad T. Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area. United States. https://doi.org/10.1186/s40168-019-0695-5
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Richardson, Miles, Gottel, Neil, Gilbert, Jack A., Gordon, Julian, Gandhi, Prasanthi, Reboulet, Rachel, and Hampton-Marcell, Jarrad T. Mon . "Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area". United States. https://doi.org/10.1186/s40168-019-0695-5. https://www.osti.gov/servlets/purl/1627052.
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@article{osti_1627052,
title = {Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area},
author = {Richardson, Miles and Gottel, Neil and Gilbert, Jack A. and Gordon, Julian and Gandhi, Prasanthi and Reboulet, Rachel and Hampton-Marcell, Jarrad T.},
abstractNote = {The particulate and biological components of indoor air have a substantial impact on human health, especially immune respiratory conditions such as asthma. To better explore the relationship between allergens, the microbial community, and the indoor living environment, we sampled the bedrooms of 65 homes in the Chicago area using 23the patient-friendly Inspirotec electrokinetic air sampling device, which collects airborne particles for characterization of both allergens and microbial DNA. The sampling device captured sufficient microbial material to enable 16S rRNA amplicon sequencing data to be generated for every sample in the study. Neither the presence of HEPA filters nor the height at which the air sampling device was placed had any influence on the microbial community profile. A core microbiota of 31 OTUs was present in more than three quarters of the samples, comprising around 45% of the relative sequence counts in each bedroom. The most abundant single organisms were Staphylococcus, with other core taxa both human and outdoor-associated. Bacterial alpha diversity was significantly increased in bedrooms that reported having open windows, those with flowering plants in the vicinity, and those in homes occupied by dogs. Porphyromonas, Moraxella, Sutterella, and Clostridium, along with family Neisseraceae, were significantly enriched in homes with dogs; interestingly, cats did not show a significant impact on microbial diversity or relative abundance. While dog allergen load was significantly correlated with bacterial alpha diversity, the taxa that significantly correlated with allergen burden did not exclusively overlap with those enriched in homes with dogs. Alternaria allergen load was positively correlated with bacterial alpha diversity, while Aspergillus allergen load was negatively correlated. The Alternaria allergen load was also significantly correlated with open windows. Microbial communities were significantly differentiated between rural, suburban, and urban homes and houses that were physically closer to each other maintained significantly more similar microbiota. We have demonstrated that it is possible to determine significant associations between allergen burden and the microbiota in air from the same sample and that these associations relate to the characteristics of the home and neighborhoods.},
doi = {10.1186/s40168-019-0695-5},
journal = {Microbiome},
number = 1,
volume = 7,
place = {United States},
year = {Mon Jun 03 00:00:00 EDT 2019},
month = {Mon Jun 03 00:00:00 EDT 2019}
}
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Publisher's Version of Record
https://doi.org/10.1186/s40168-019-0695-5
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Figures / Tables:

Table 1 Table 1: Correlating allergen load with the bacterial Shannon diversity metric
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Bedroom exposure to airborne allergens in the Chicago area using a patient-operated sampling device
journal, August 2018

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  • Annals of Allergy, Asthma & Immunology, Vol. 121, Issue 2
  • DOI: 10.1016/j.anai.2018.05.024

Seasonal variability in airborne bacterial communities at a high-elevation site
journal, April 2012

Man's best friend? The effect of pet ownership on house dust microbial communities
journal, August 2010

  • Fujimura, Kei E.; Johnson, Christine C.; Ownby, Dennis R.
  • Journal of Allergy and Clinical Immunology, Vol. 126, Issue 2
  • DOI: 10.1016/j.jaci.2010.05.042

Does diversity of environmental microbial exposure matter for the occurrence of allergy and asthma?
journal, July 2012

Indoor Environmental Interventions for Furry Pet Allergens, Pest Allergens, and Mold: Looking to the Future
journal, January 2018

  • Ahluwalia, Sharon K.; Matsui, Elizabeth C.
  • The Journal of Allergy and Clinical Immunology: In Practice, Vol. 6, Issue 1
  • DOI: 10.1016/j.jaip.2017.10.009

Indoor Emissions as a Primary Source of Airborne Allergenic Fungal Particles in Classrooms
journal, April 2015

  • Yamamoto, Naomichi; Hospodsky, Denina; Dannemiller, Karen C.
  • Environmental Science & Technology, Vol. 49, Issue 8
  • DOI: 10.1021/es506165z

Architectural design influences the diversity and structure of the built environment microbiome
journal, January 2012

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  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 1, p. 299-304
  • DOI: 10.1073/pnas.0608255104

Sampling and Retention Efficiencies of Batch-Type Liquid-Based Bioaerosol Samplers
journal, August 2010

  • Kesavan, Jana; Schepers, Deborah; McFarland, Andrew R.
  • Aerosol Science and Technology, Vol. 44, Issue 10
  • DOI: 10.1080/02786826.2010.497513

Pathogenic Aspergillus Species Recovered from a Hospital Water System: A 3-Year Prospective Study
journal, March 2002

  • Anaissie, Elias J.; Stratton, Shawna L.; Dignani, M. Cecilia
  • Clinical Infectious Diseases, Vol. 34, Issue 6
  • DOI: 10.1086/338958

Cleaning Patient Shower Facilities: A Novel Approach to Reducing Patient Exposure to Aerosolized Aspergillus Species and Other Opportunistic Molds
journal, October 2002

  • Anaissie, Elias J.; Stratton, Shawna L.; Dignani, Maria Cecilia
  • Clinical Infectious Diseases, Vol. 35, Issue 8
  • DOI: 10.1086/342305

Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes: Household air bacteria differ from occupant skin
journal, June 2015

  • Wilkins, David; Leung, Marcus HY; Lee, Patrick KH
  • Environmental Microbiology, Vol. 18, Issue 6
  • DOI: 10.1111/1462-2920.12889

Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source
journal, May 2013

  • Meadow, J. F.; Altrichter, A. E.; Kembel, S. W.
  • Indoor Air, Vol. 24, Issue 1
  • DOI: 10.1111/ina.12047

VEGAN, a package of R functions for community ecology
journal, April 2003

Topographical and Temporal Diversity of the Human Skin Microbiome
journal, May 2009

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014

A simple novel device for air sampling by electrokinetic capture
journal, December 2015

Respiratory and Allergic Health Effects of Dampness, Mold, and Dampness-Related Agents: A Review of the Epidemiologic Evidence
journal, June 2011

  • Mendell, Mark J.; Mirer, Anna G.; Cheung, Kerry
  • Environmental Health Perspectives, Vol. 119, Issue 6
  • DOI: 10.1289/ehp.1002410

Human Occupancy as a Source of Indoor Airborne Bacteria
journal, April 2012

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